PMC:7321036 / 85216-85793 JSONTXT

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T186","span":{"begin":232,"end":268},"obj":"NCBITaxon:9606"},{"id":"T187","span":{"begin":375,"end":425},"obj":"SP_6;NCBITaxon:9606"},{"id":"T188","span":{"begin":488,"end":549},"obj":"SO:0000704"}],"text":"Raw mass spectrometry data from each DDA dataset were used to build separate libraries for DIA searches using the Pulsar search engine integrated into Spectronaut version 13.12.200217.43655 (Bruderer et al., 2015) by searching against a database of Uniprot Chlorocebus sequences (19,136 proteins, downloaded April 3, 2020) and 29 SARS-CoV-2 protein sequences translated from genomic sequence downloaded from GISAID (accession EPI_ISL_406596, downloaded April 7, 2020) with two mutations (G22661T Spike V367F and G26144T ORF3a G251V) detected by RNASeq analysis of virus stocks."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T619","span":{"begin":287,"end":295},"obj":"Body_part"},{"id":"T620","span":{"begin":341,"end":348},"obj":"Body_part"}],"attributes":[{"id":"A619","pred":"fma_id","subj":"T619","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A620","pred":"fma_id","subj":"T620","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Raw mass spectrometry data from each DDA dataset were used to build separate libraries for DIA searches using the Pulsar search engine integrated into Spectronaut version 13.12.200217.43655 (Bruderer et al., 2015) by searching against a database of Uniprot Chlorocebus sequences (19,136 proteins, downloaded April 3, 2020) and 29 SARS-CoV-2 protein sequences translated from genomic sequence downloaded from GISAID (accession EPI_ISL_406596, downloaded April 7, 2020) with two mutations (G22661T Spike V367F and G26144T ORF3a G251V) detected by RNASeq analysis of virus stocks."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T343","span":{"begin":91,"end":94},"obj":"Disease"},{"id":"T344","span":{"begin":330,"end":338},"obj":"Disease"}],"attributes":[{"id":"A343","pred":"mondo_id","subj":"T343","obj":"http://purl.obolibrary.org/obo/MONDO_0022963"},{"id":"A344","pred":"mondo_id","subj":"T344","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Raw mass spectrometry data from each DDA dataset were used to build separate libraries for DIA searches using the Pulsar search engine integrated into Spectronaut version 13.12.200217.43655 (Bruderer et al., 2015) by searching against a database of Uniprot Chlorocebus sequences (19,136 proteins, downloaded April 3, 2020) and 29 SARS-CoV-2 protein sequences translated from genomic sequence downloaded from GISAID (accession EPI_ISL_406596, downloaded April 7, 2020) with two mutations (G22661T Spike V367F and G26144T ORF3a G251V) detected by RNASeq analysis of virus stocks."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T1188","span":{"begin":235,"end":236},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1189","span":{"begin":564,"end":569},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"}],"text":"Raw mass spectrometry data from each DDA dataset were used to build separate libraries for DIA searches using the Pulsar search engine integrated into Spectronaut version 13.12.200217.43655 (Bruderer et al., 2015) by searching against a database of Uniprot Chlorocebus sequences (19,136 proteins, downloaded April 3, 2020) and 29 SARS-CoV-2 protein sequences translated from genomic sequence downloaded from GISAID (accession EPI_ISL_406596, downloaded April 7, 2020) with two mutations (G22661T Spike V367F and G26144T ORF3a G251V) detected by RNASeq analysis of virus stocks."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T458","span":{"begin":37,"end":40},"obj":"Chemical"},{"id":"T460","span":{"begin":287,"end":295},"obj":"Chemical"},{"id":"T461","span":{"begin":341,"end":348},"obj":"Chemical"}],"attributes":[{"id":"A458","pred":"chebi_id","subj":"T458","obj":"http://purl.obolibrary.org/obo/CHEBI_28139"},{"id":"A459","pred":"chebi_id","subj":"T458","obj":"http://purl.obolibrary.org/obo/CHEBI_91207"},{"id":"A460","pred":"chebi_id","subj":"T460","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A461","pred":"chebi_id","subj":"T461","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"Raw mass spectrometry data from each DDA dataset were used to build separate libraries for DIA searches using the Pulsar search engine integrated into Spectronaut version 13.12.200217.43655 (Bruderer et al., 2015) by searching against a database of Uniprot Chlorocebus sequences (19,136 proteins, downloaded April 3, 2020) and 29 SARS-CoV-2 protein sequences translated from genomic sequence downloaded from GISAID (accession EPI_ISL_406596, downloaded April 7, 2020) with two mutations (G22661T Spike V367F and G26144T ORF3a G251V) detected by RNASeq analysis of virus stocks."}

{"project":"LitCovid-PubTator","denotations":[{"id":"1892","span":{"begin":520,"end":525},"obj":"Gene"},{"id":"1894","span":{"begin":496,"end":501},"obj":"Gene"},{"id":"1895","span":{"begin":330,"end":340},"obj":"Species"},{"id":"1896","span":{"begin":570,"end":576},"obj":"Species"},{"id":"1897","span":{"begin":257,"end":268},"obj":"Species"},{"id":"1902","span":{"begin":488,"end":495},"obj":"Mutation"},{"id":"1903","span":{"begin":502,"end":507},"obj":"Mutation"},{"id":"1904","span":{"begin":512,"end":519},"obj":"Mutation"},{"id":"1905","span":{"begin":526,"end":531},"obj":"Mutation"}],"attributes":[{"id":"A1892","pred":"tao:has_database_id","subj":"1892","obj":"Gene:43740569"},{"id":"A1894","pred":"tao:has_database_id","subj":"1894","obj":"Gene:43740568"},{"id":"A1895","pred":"tao:has_database_id","subj":"1895","obj":"Tax:2697049"},{"id":"A1896","pred":"tao:has_database_id","subj":"1896","obj":"Tax:3724"},{"id":"A1897","pred":"tao:has_database_id","subj":"1897","obj":"Tax:60711"},{"id":"A1902","pred":"tao:has_standard_notation","subj":"1902","obj":"g.22661G\u003eT"},{"id":"A1903","pred":"tao:has_standard_notation","subj":"1903","obj":"p.V367F"},{"id":"A1904","pred":"tao:has_standard_notation","subj":"1904","obj":"g.26144G\u003eT"},{"id":"A1905","pred":"tao:has_standard_notation","subj":"1905","obj":"p.G251V"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Raw mass spectrometry data from each DDA dataset were used to build separate libraries for DIA searches using the Pulsar search engine integrated into Spectronaut version 13.12.200217.43655 (Bruderer et al., 2015) by searching against a database of Uniprot Chlorocebus sequences (19,136 proteins, downloaded April 3, 2020) and 29 SARS-CoV-2 protein sequences translated from genomic sequence downloaded from GISAID (accession EPI_ISL_406596, downloaded April 7, 2020) with two mutations (G22661T Spike V367F and G26144T ORF3a G251V) detected by RNASeq analysis of virus stocks."}

{"project":"LitCovid-sentences","denotations":[{"id":"T769","span":{"begin":0,"end":577},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Raw mass spectrometry data from each DDA dataset were used to build separate libraries for DIA searches using the Pulsar search engine integrated into Spectronaut version 13.12.200217.43655 (Bruderer et al., 2015) by searching against a database of Uniprot Chlorocebus sequences (19,136 proteins, downloaded April 3, 2020) and 29 SARS-CoV-2 protein sequences translated from genomic sequence downloaded from GISAID (accession EPI_ISL_406596, downloaded April 7, 2020) with two mutations (G22661T Spike V367F and G26144T ORF3a G251V) detected by RNASeq analysis of virus stocks."}

{"project":"2_test","denotations":[{"id":"32645325-25724911-20773110","span":{"begin":208,"end":212},"obj":"25724911"}],"text":"Raw mass spectrometry data from each DDA dataset were used to build separate libraries for DIA searches using the Pulsar search engine integrated into Spectronaut version 13.12.200217.43655 (Bruderer et al., 2015) by searching against a database of Uniprot Chlorocebus sequences (19,136 proteins, downloaded April 3, 2020) and 29 SARS-CoV-2 protein sequences translated from genomic sequence downloaded from GISAID (accession EPI_ISL_406596, downloaded April 7, 2020) with two mutations (G22661T Spike V367F and G26144T ORF3a G251V) detected by RNASeq analysis of virus stocks."}